| | Molecular Biology Transcriptional regulation of the Drosophila moira and osa genes by the DREF pathway Kumi Nakamura, Hiroyuki Ida, and Masamitsu Yamaguchi PMCID: PMC2475616 Differential binding of quadruplex structures of muscle-specific genes regulatory sequences by MyoD, MRF4 and myogenin Anat Yafe, Jeny Shklover, Pnina Weisman-Shomer, Eyal Bengal, and Michael Fry PMCID: PMC2475631 The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions Tomohiro Shimada, Akira Ishihama, Stephen J. W. Busby, and David C. Grainger PMCID: PMC2475637 DNA protection by histone-like protein HU from the hyperthermophilic eubacterium Thermotoga maritima Anirban Mukherjee, Abimbola O. Sokunbi, and Anne Grove PMCID: PMC2475624 Eukaryotic HMGB proteins as replacements for HU in E. coli repression loop formation Nicole A. Becker, Jason D. Kahn, and L. James Maher, III PMCID: PMC2475640 Alkylation damage causes MMR-dependent chromosomal instability in vertebrate embryos Harma Feitsma, Alper Akay, and Edwin Cuppen PMCID: PMC2475609 A comparative analysis of Dmc1 and Rad51 nucleoprotein filaments Sean D. Sheridan, Xiong Yu, Robyn Roth, John E. Heuser, Michael G. Sehorn, Patrick Sung, Edward H. Egelman, and Douglas K. Bishop PMCID: PMC2475612 TSA downregulates Wilms tumor gene 1 (Wt1) expression at multiple levels Mohammad Shahidul Makki, Thorsten Heinzel, and Christoph Englert PMCID: PMC2475629 Hierarchy of nonhomologous end-joining, single-strand annealing and gene conversion at site-directed DNA double-strand breaks Wael Y. Mansour, Sabine Schumacher, Raphael Rosskopf, Tim Rhein, Filip Schmidt-Petersen, Fruszina Gatzemeier, Friedrich Haag, Kerstin Borgmann, Henning Willers, and Jochen Dahm-Daphi PMCID: PMC2475611 Structural and functional analyses of the DMC1-M200V polymorphism found in the human population Juri Hikiba, Kouji Hirota, Wataru Kagawa, Shukuko Ikawa, Takashi Kinebuchi, Isao Sakane, Yoshimasa Takizawa, Shigeyuki Yokoyama, Béatrice Mandon-Pépin, Alain Nicolas, Takehiko Shibata, Kunihiro Ohta, and Hitoshi Kurumizaka PMCID: PMC2475644 RNA Inhibition of 3′ modification of small RNAs in virus-infected plants require spatial and temporal co-expression of small RNAs and viral silencing-suppressor proteins Rita Lózsa, Tibor Csorba, Lóránt Lakatos, and József Burgyán PMCID: PMC2475607 Studies on Methanocaldococcus jannaschii RNase P reveal insights into the roles of RNA and protein cofactors in RNase P catalysis Dileep K. Pulukkunat and Venkat Gopalan PMCID: PMC2475606 Cytosine ribose flexibility in DNA: a combined NMR 13C spin relaxation and molecular dynamics simulation study Elke Duchardt, Lennart Nilsson, and Jürgen Schleucher PMCID: PMC2475628 Structural Biology Structural change in a B-DNA helix with hydrostatic pressure David J. Wilton, Mahua Ghosh, K. V. A. Chary, Kazuyuki Akasaka, and Mike P. Williamson PMCID: PMC2475645 Structural polymorphism of intramolecular quadruplex of human telomeric DNA: effect of cations, quadruplex-binding drugs and flanking sequences Timur I. Gaynutdinov, Ronald D. Neumann, and Igor G. Panyutin PMCID: PMC2475613 The modulation of topoisomerase I-mediated DNA cleavage and the induction of DNA–topoisomerase I crosslinks by crotonaldehyde-derived DNA adducts Thomas S. Dexheimer, Albena Kozekova, Carmelo J. Rizzo, Michael P. Stone, and Yves Pommier PMCID: PMC2475617 Kinetics and mechanism of K+- and Na+-induced folding of models of human telomeric DNA into G-quadruplex structures Robert D. Gray and Jonathan B. Chaires PMCID: PMC2475619 The antiparallel loops in gal DNA Giuseppe Lia, Szabolcs Semsey, Dale E. A. Lewis, Sankar Adhya, David Bensimon, David Dunlap, and Laura Finzi PMCID: PMC2475638 Survey and Summary Mechanisms and strategies for effective delivery of antisense and siRNA oligonucleotides Rudy Juliano, Md. Rowshon Alam, Vidula Dixit, and Hyumin Kang PMCID: PMC2475625 Genomics Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex Henri-Marc Bourbon PMCID: PMC2475620 Cis-regulatory modules in the mammalian liver: composition depends on strength of Foxa2 consensus site Geetu Tuteja, Shane T. Jensen, Peter White, and Klaus H. Kaestner PMCID: PMC2475634 Methods Online Efficient cytosolic delivery of molecular beacon conjugates and flow cytometric analysis of target RNA Antony K. Chen, Mark A. Behlke, and Andrew Tsourkas PMCID: PMC2475621 Single-molecule imaging of full protein synthesis by immobilized ribosomes Sotaro Uemura, Ryo Iizuka, Taro Ueno, Yoshihiro Shimizu, Hideki Taguchi, Takuya Ueda, Joseph D. Puglisi, and Takashi Funatsu PMCID: PMC2475623 Nuclear delivery of NFκB-assisted DNA/polymer complexes: plasmid DNA quantitation by confocal laser scanning microscopy and evidence of nuclear polyplexes by FRET imaging Gilles Breuzard, Magdalena Tertil, Cristine Gonçalves, Hervé Cheradame, Philippe Géguan, Chantal Pichon, and Patrick Midoux PMCID: PMC2475639 Inversing the natural hydrogen bonding rule to selectively amplify GC-rich ADAR-edited RNAs Rodolphe Suspène, Myrtille Renard, Michel Henry, Denise Guétard, David Puyraimond-Zemmour, Agnès Billecocq, Michèle Bouloy, Frederic Tangy, Jean-Pierre Vartanian, and Simon Wain-Hobson PMCID: PMC2475633 Minimally invasive determination of mRNA concentration in single living bacteria Călin C. Guet, Luke Bruneaux, Taejin L. Min, Dan Siegal-Gaskins, Israel Figueroa, Thierry Emonet, and Philippe Cluzel PMCID: PMC2475643 Improved assay-dependent searching of nucleic acid sequence databases Jason D. Gans and Murray Wolinsky PMCID: PMC2475610 Development of a single tube 640-plex genotyping method for detection of nucleic acid variations on microarrays Kaarel Krjutškov, Reidar Andreson, Reedik Mägi, Tiit Nikopensius, Andrey Khrunin, Evelin Mihailov, Veronika Tammekivi, Helena Sork, Maido Remm, and Andres Metspalu PMCID: PMC2475630 Promoter library designed for fine-tuned gene expression in Pichia pastoris Franz S. Hartner, Claudia Ruth, David Langenegger, Sabrina N. Johnson, Petr Hyka, Geoffrey P. Lin-Cereghino, Joan Lin-Cereghino, Karin Kovar, James M. Cregg, and Anton Glieder PMCID: PMC2475614 Computational Biology DBD-Hunter: a knowledge-based method for the prediction of DNA–protein interactions Mu Gao and Jeffrey Skolnick PMCID: PMC2475642 Computational design of orthogonal ribosomes Lon M. Chubiz and Christopher V. Rao PMCID: PMC2475622 Associating transcription factor-binding site motifs with target GO terms and target genes Mikael Bodén and Timothy L. Bailey PMCID: PMC2475605 Extracting sequence features to predict protein–DNA interactions: a comparative study Qing Zhou and Jun S. Liu PMCID: PMC2475627 Nucleic Acid Enzymes Mechanism of double-base lesion bypass catalyzed by a Y-family DNA polymerase Jessica A. Brown, Sean A. Newmister, Kevin A. Fiala, and Zucai Suo PMCID: PMC2475632 A motif in the C-terminal domain of ϕC31 integrase controls the directionality of recombination Paul A. Rowley, Matthew C. A. Smith, Ellen Younger, and Margaret C. M. Smith PMCID: PMC2475636 Characterization of a replicative DNA polymerase mutant with reduced fidelity and increased translesion synthesis capacity Xuejun Zhong, Lars C. Pedersen, and Thomas A. Kunkel PMCID: PMC2475618 Development of a single-chain, quasi-dimeric zinc-finger nuclease for the selective degradation of mutated human mitochondrial DNA Michal Minczuk, Monika A. Papworth, Jeffrey C. Miller, Michael P. Murphy, and Aaron Klug PMCID: PMC2475635 A RecB-family nuclease motif in the Type I restriction endonuclease EcoR124I Eva Šišáková, Louise K. Stanley, Marie Weiserová, and Mark D. Szczelkun PMCID: PMC2475608 Template-directed addition of nucleosides to DNA by the BfiI restriction enzyme Giedrius Sasnauskas, Bernard A. Connolly, Stephen E. Halford, and Virginijus Siksnys PMCID: PMC2475615 A mechanism for DNA-PK activation requiring unique contributions from each strand of a DNA terminus and implications for microhomology-mediated nonhomologous DNA end joining Katherine S. Pawelczak and John J. Turchi PMCID: PMC2475626 Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA Isabelle Bonnet, Andreas Biebricher, Pierre-Louis Porté, Claude Loverdo, Olivier Bénichou, Raphaël Voituriez, Christophe Escudé, Wolfgang Wende, Alfred Pingoud, and Pierre Desbiolles PMCID: PMC2475641 |
